This paper describes an effective approach to order gold nanorods (NRs) within cylindrically confined microdomains of block copolymer- (BCP-) based supramolecular assemblies. Individual BCP micelles encapsulated with well-ordered NRs can be obtained by disassembling the supramolecular structures. The mismatch of binary polymer brushes with different lengths on the surface of the NRs was used to effectively improve the dispersion of the NRs within polymer matrix, due to enhanced wetting of the brushes by surrounding mismatch polymers. This enables us to quantitatively explore the location and orientation of the NRs within confined geometries. By varying the content of NRs, the aspect ratio of the NRs, or the diameter of the cylindrical BCP micelles, the orientation of the NRs within micelles can be tuned to form one-dimensional nanostrings with end-to-end organization of NRs along the micelles or with side-by-side twisted arrangement of NRs perpendicular to the micelles. UV-vis spectroscopy measurements and finite-difference time-domain (FDTD) calculations confirm that our approach provides a simple yet versatile route to tune the optical properties of the hybrid micelles by controlling the ordering of the NRs. This work provides guidelines for dispersing other functional anisotropic NPs, and lays groundwork for the fabrication of optical and electronic devices.